Tools and information for AMBER and CPPTRAJ examples
Updated: March 22, 2019
Perform lifetime analysis for specified data sets. lifetime [out <filename>] <dsetarg0> [ <dsetarg1> … ] [window <windowsize> [name <setname>]] [averageonly] [cumulative] [delta] [cut <cutoff>] [greater | less] [rawcurve] [fuzz <fuzzcut>] [nosort] [out <filename>] Write results to file named… Read More
Updated: March 25, 2019
For each given data set, calculate a curve that traces the lowest N points over specified bins. lowestcurve points <# lowest> [step <stepsize>] <dset0> [<dset1> …][out <file>] [name <setname>] <# lowest> Number of lowest points in each bin… Read More
Updated: March 25, 2019
Calculate a melting curve from given data sets assuming simple 2 state kinetics. meltcurve <dset0> [<dset1> …] [out <outfile>] [name <outsetname>] cut <cut> Calculate melting curve from input data sets (i.e. fraction ’folded’ for each data set) assuming… Read More
Updated: April 6, 2022
Perform various analyses on eigenmodes (from e.g. diagmatrix). modes {fluct|displ|corr|eigenval|trajout|rmsip} name <modesname> [name2 <modesname>] [beg <beg>] [end <end>] [bose] [factor <factor>] [calcall] [out <outfile>] [setname <name>] Options for ’trajout’: (Generate pseudo-trajectory) [trajout <name> parm <name> | parmindex <#>[trajoutfmt… Read More
Updated: March 25, 2019
Perform non-linear curve fitting for multiple input data sets. multicurve set <dset> [set <dset> …]<dset> { <equation> | name <dsname> nexp <m> [form {mexp|mexpk|mexpk_penalty} } [AX=<value> …] [out <outfile>] [resultsout <results>] [maxit <max iterations>] [tol <tolerance>] [outxbins <NX>… Read More
Updated: November 29, 2022
Calculate 1D histograms (optionally with a kernel N 1D scalar density estimator) from multiple input data sets. multihist [out <filename>] [name <dsname>] [norm | normint] [kde] [min <min>] [max <max>] [step <step>] [bins <bins>] [free <T>]<dsetarg0> [ <dsetarg1>… Read More
Updated: March 25, 2019
Calculate and plot the average phi and psi values from input dihedral data sets. phipsi <dsarg0> [<dsarg1> …] resrange <range> [out <file>] <dsargX> Argument selecting data sets. Can specify more than 1. resrange <range> Residue range to use… Read More
Updated: March 25, 2019
Perform linear regression on multiple input data sets. regress <dset0> [<dset1> …] [name <name>] [nx <nxvals>][out <filename>] [statsout <filename>] dsetX Data set(s) to perform linear regression for. name <name> Data set name for resulting linear fits. nx <nxvals>… Read More
Updated: March 25, 2019
Calculate various statistics from a replica log data set. remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx | repidx][stats [statsout <file>] [printtrips] [reptime <file>]] [lifetime <file>] [reptimeslope <n> reptimeslopeout <file>] [acceptout <file>] [name <setname>] <remlog dataset> Previously… Read More
Updated: April 12, 2023
Calculate 2D RMSD between frames in 1 or 2 COORDS data sets. rms2d [crdset <crd set>] [<name>] [<mask>] [out <filename>][dme | nofit | srmsd] [mass][reftraj <traj> [parm <parmname> | parmindex <parm#>] [<refmask>]][corr <corrfilename>] [crdset <crd set>] Name of… Read More
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